/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkSliceCubes.cxx

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#include "vtkSliceCubes.h"

#include "vtkByteSwap.h"
#include "vtkCharArray.h"
#include "vtkDoubleArray.h"
#include "vtkFloatArray.h"
#include "vtkImageData.h"
#include "vtkIntArray.h"
#include "vtkLongArray.h"
#include "vtkMarchingCubesTriangleCases.h"
#include "vtkMath.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkShortArray.h"
#include "vtkUnsignedCharArray.h"
#include "vtkUnsignedIntArray.h"
#include "vtkUnsignedLongArray.h"
#include "vtkUnsignedShortArray.h"
#include "vtkVolumeReader.h"
#include <vtksys/SystemTools.hxx>

vtkStandardNewMacro(vtkSliceCubes);

vtkCxxSetObjectMacro(vtkSliceCubes, Reader, vtkVolumeReader);

// Description:
// Construct with nullptr reader, output FileName specification, and limits
// FileName.
vtkSliceCubes::vtkSliceCubes()
{
  this->Reader = nullptr;
  this->FileName = nullptr;
  this->LimitsFileName = nullptr;
  this->Value = 0.0;
}

vtkSliceCubes::~vtkSliceCubes()
{
  delete[] this->FileName;
  delete[] this->LimitsFileName;
  this->SetReader(nullptr);
}

// Description:
// Method causes object to read slices and generate isosurface.
void vtkSliceCubes::Update()
{
  this->Execute();
}

// Calculate the gradient using central difference.
// NOTE: We calculate the negative of the gradient for efficiency
template <class T>
void ComputePointGradient(
  int i, int j, int k, int dims[3], double Spacing[3], double n[3], T* s0, T* s1, T* s2)
{
  double sp, sm;

  // x-direction
  if (i == 0)
  {
    sp = s1[i + 1 + j * dims[0]];
    sm = s1[i + j * dims[0]];
    n[0] = (sm - sp) / Spacing[0];
  }
  else if (i == (dims[0] - 1))
  {
    sp = s1[i + j * dims[0]];
    sm = s1[i - 1 + j * dims[0]];
    n[0] = (sm - sp) / Spacing[0];
  }
  else
  {
    sp = s1[i + 1 + j * dims[0]];
    sm = s1[i - 1 + j * dims[0]];
    n[0] = 0.5 * (sm - sp) / Spacing[0];
  }

  // y-direction
  if (j == 0)
  {
    sp = s1[i + (j + 1) * dims[0]];
    sm = s1[i + j * dims[0]];
    n[1] = (sm - sp) / Spacing[1];
  }
  else if (j == (dims[1] - 1))
  {
    sp = s1[i + j * dims[0]];
    sm = s1[i + (j - 1) * dims[0]];
    n[1] = (sm - sp) / Spacing[1];
  }
  else

  {
    sp = s1[i + (j + 1) * dims[0]];
    sm = s1[i + (j - 1) * dims[0]];
    n[1] = 0.5 * (sm - sp) / Spacing[1];
  }

  // z-direction
  // z-direction
  if (k == 0)
  {
    sp = s2[i + j * dims[0]];
    sm = s1[i + j * dims[0]];
    n[2] = (sm - sp) / Spacing[2];
  }
  else if (k == (dims[2] - 1))
  {
    sp = s1[i + j * dims[0]];
    sm = s0[i + j * dims[0]];
    n[2] = (sm - sp) / Spacing[2];
  }
  else
  {
    sp = s2[i + j * dims[0]];
    sm = s0[i + j * dims[0]];
    n[2] = 0.5 * (sm - sp) / Spacing[2];
  }
}

template <class T, class S>
int vtkSliceCubesContour(T* slice, S* scalars, int imageRange[2], int dims[3], double origin[3],
  double Spacing[3], double value, double xmin[3], double xmax[3], FILE* outFP,
  vtkVolumeReader* reader, bool debug)
{
  S *slice0scalars = nullptr, *slice1scalars = nullptr;
  S *slice2scalars, *slice3scalars;
  T *slice0, *slice1, *slice2, *slice3;
  vtkImageData* sp;
  vtkDoubleArray* doubleScalars = nullptr;
  int numTriangles = 0, numComp = 0;
  double s[8];
  int i, j, k, idx, jOffset, ii, index, *vert, jj, sliceSize = 0;
  static const int CASE_MASK[8] = { 1, 2, 4, 8, 16, 32, 64, 128 };
  vtkMarchingCubesTriangleCases *triCase, *triCases;
  EDGE_LIST* edge;
  double pts[8][3], grad[8][3];
  double t, *x1, *x2, *n1, *n2;
  double xp, yp, zp;
  float point[6];
  static int edges[12][2] = { { 0, 1 }, { 1, 2 }, { 3, 2 }, { 0, 3 }, { 4, 5 }, { 5, 6 }, { 7, 6 },
    { 4, 7 }, { 0, 4 }, { 1, 5 }, { 3, 7 }, { 2, 6 } };

  triCases = vtkMarchingCubesTriangleCases::GetCases();

  if (slice == nullptr) // have to do conversion to double slice-by-slice
  {
    sliceSize = dims[0] * dims[1];
    doubleScalars = vtkDoubleArray::New();
    doubleScalars->Allocate(sliceSize);
  }

  slice2scalars = scalars;
  slice2scalars->Register(nullptr);

  if (debug)
    vtkGenericWarningMacro(<< "  Slice# " << imageRange[0]);

  if (slice2scalars == nullptr)
  {
    return 0;
  }
  if (slice != nullptr)
  {
    slice1 = slice2 = slice2scalars->GetPointer(0);
  }
  else
  { // get as double
    numComp = scalars->GetNumberOfComponents();
    slice2scalars->GetData(0, sliceSize - 1, 0, numComp - 1, doubleScalars);
    slice1 = slice2 = (T*)doubleScalars->GetPointer(0);
  }

  sp = reader->GetImage(imageRange[0] + 1);
  slice3scalars = (S*)sp->GetPointData()->GetScalars();
  slice3scalars->Register(nullptr);
  sp->Delete();

  if (debug)
    vtkGenericWarningMacro(<< "  Slice# " << imageRange[0] + 1);

  if (slice != nullptr)
  {
    slice3 = slice3scalars->GetPointer(0);
  }
  else
  { // get as double: cast is ok because this code is only executed for double type
    slice3scalars->GetData(0, sliceSize - 1, 0, numComp - 1, doubleScalars);
    slice3 = (T*)doubleScalars->GetPointer(0);
  }

  if (!slice2 || !slice3)
  {
    vtkGenericWarningMacro(<< "Cannot allocate data!");
    return 0;
  }

  // Generate triangles and normals from slices
  for (k = 0; k < (dims[2] - 1); k++)
  {

    // swap things around
    if (slice0scalars != nullptr)
    {
      slice0scalars->Delete();
    }
    slice0scalars = slice1scalars;
    slice0 = slice1;
    slice1scalars = slice2scalars;
    slice1 = slice2;
    slice2scalars = slice3scalars;
    slice2 = slice3;
    if (k < (dims[2] - 2))
    {
      if (debug)
        vtkGenericWarningMacro(<< "  Slice# " << imageRange[0] + k + 2);
      sp = reader->GetImage(imageRange[0] + k + 2);
      slice3scalars = (S*)sp->GetPointData()->GetScalars();
      if (slice3scalars == nullptr)
      {
        vtkGenericWarningMacro(<< "Can't read all the requested slices");
        goto PREMATURE_TERMINATION;
      }
      slice3scalars->Register(nullptr);
      sp->Delete();
      if (slice != nullptr)
      {
        slice3 = slice3scalars->GetPointer(0);
      }
      else
      { // get as double
        slice3scalars->GetData(0, sliceSize - 1, 0, numComp - 1, doubleScalars);
        slice3 = (T*)doubleScalars->GetPointer(0);
      }
    }

    pts[0][2] = origin[2] + k * Spacing[2];
    zp = origin[2] + (k + 1) * Spacing[2];
    for (j = 0; j < (dims[1] - 1); j++)
    {
      jOffset = j * dims[0];
      pts[0][1] = origin[1] + j * Spacing[1];
      yp = origin[1] + (j + 1) * Spacing[1];
      for (i = 0; i < (dims[0] - 1); i++)
      {
        // get scalar values
        idx = i + jOffset;
        s[0] = slice1[idx];
        s[1] = slice1[idx + 1];
        s[2] = slice1[idx + 1 + dims[0]];
        s[3] = slice1[idx + dims[0]];
        s[4] = slice2[idx];
        s[5] = slice2[idx + 1];
        s[6] = slice2[idx + 1 + dims[0]];
        s[7] = slice2[idx + dims[0]];

        // Build the case table
        for (ii = 0, index = 0; ii < 8; ii++)
        {
          if (s[ii] >= value)
          {
            index |= CASE_MASK[ii];
          }
        }

        if (index == 0 || index == 255) // no surface
        {
          continue;
        }
        // create voxel points
        pts[0][0] = origin[0] + i * Spacing[0];
        xp = origin[0] + (i + 1) * Spacing[0];

        pts[1][0] = xp;
        pts[1][1] = pts[0][1];
        pts[1][2] = pts[0][2];

        pts[2][0] = xp;
        pts[2][1] = yp;
        pts[2][2] = pts[0][2];

        pts[3][0] = pts[0][0];
        pts[3][1] = yp;
        pts[3][2] = pts[0][2];

        pts[4][0] = pts[0][0];
        pts[4][1] = pts[0][1];
        pts[4][2] = zp;

        pts[5][0] = xp;
        pts[5][1] = pts[0][1];
        pts[5][2] = zp;

        pts[6][0] = xp;
        pts[6][1] = yp;
        pts[6][2] = zp;

        pts[7][0] = pts[0][0];
        pts[7][1] = yp;
        pts[7][2] = zp;

        // create gradients
        ComputePointGradient(i, j, k, dims, Spacing, grad[0], slice0, slice1, slice2);
        ComputePointGradient(i + 1, j, k, dims, Spacing, grad[1], slice0, slice1, slice2);
        ComputePointGradient(i + 1, j + 1, k, dims, Spacing, grad[2], slice0, slice1, slice2);
        ComputePointGradient(i, j + 1, k, dims, Spacing, grad[3], slice0, slice1, slice2);
        ComputePointGradient(i, j, k + 1, dims, Spacing, grad[4], slice1, slice2, slice3);
        ComputePointGradient(i + 1, j, k + 1, dims, Spacing, grad[5], slice1, slice2, slice3);
        ComputePointGradient(i + 1, j + 1, k + 1, dims, Spacing, grad[6], slice1, slice2, slice3);
        ComputePointGradient(i, j + 1, k + 1, dims, Spacing, grad[7], slice1, slice2, slice3);

        triCase = triCases + index;
        edge = triCase->edges;

        for (; edge[0] > -1; edge += 3)
        {
          for (ii = 0; ii < 3; ii++) // insert triangle
          {
            vert = edges[edge[ii]];
            t = (value - s[vert[0]]) / (s[vert[1]] - s[vert[0]]);
            x1 = pts[vert[0]];
            x2 = pts[vert[1]];
            n1 = grad[vert[0]];
            n2 = grad[vert[1]];
            for (jj = 0; jj < 3; jj++)
            {
              point[jj] = x1[jj] + t * (x2[jj] - x1[jj]);
              point[jj + 3] = n1[jj] + t * (n2[jj] - n1[jj]);
              if (point[jj] < xmin[jj])
              {
                xmin[jj] = point[jj];
              }
              if (point[jj] > xmax[jj])
              {
                xmax[jj] = point[jj];
              }
            }
            vtkMath::Normalize(point + 3);
            // swap bytes if necessary
            bool status = vtkByteSwap::SwapWrite4BERange(point, 6, outFP);
            if (!status)
            {
              vtkGenericWarningMacro(<< "SwapWrite failed!");
            }
          }
          numTriangles++;
        } // for each triangle
      }   // for i
    }     // for j
  }       // for k

// Close things down
PREMATURE_TERMINATION:

  fclose(outFP);
  if (slice == nullptr)
  {
    doubleScalars->Delete();
  }
  if (slice0scalars && slice0scalars != slice1scalars)
  {
    slice0scalars->Delete();
  }
  if (slice3scalars && slice3scalars != slice2scalars)
  {
    slice3scalars->Delete();
  }
  if (slice1scalars)
  {
    slice1scalars->Delete();
  }
  slice2scalars->Delete();

  return numTriangles;
}

void vtkSliceCubes::Execute()
{
  FILE* outFP;
  vtkImageData* tempStructPts;
  vtkDataArray* inScalars;
  int dims[3], imageRange[2];
  double xmin[3], xmax[3];
  double origin[3], Spacing[3];

  // check input/initialize
  vtkDebugMacro(<< "Executing slice cubes");
  if (this->Reader == nullptr)
  {
    vtkErrorMacro(<< "No reader specified...can't generate isosurface");
    return;
  }

  if (this->FileName == nullptr)
  {
    vtkErrorMacro(<< "No FileName specified...can't output isosurface");
    return;
  }

  if ((outFP = vtksys::SystemTools::Fopen(this->FileName, "wb")) == nullptr)
  {
    vtkErrorMacro(<< "Cannot open specified output file...");
    return;
  }

  // get image dimensions from the readers first slice
  this->Reader->GetImageRange(imageRange);
  tempStructPts = this->Reader->GetImage(imageRange[0]);
  tempStructPts->GetDimensions(dims);
  tempStructPts->GetOrigin(origin);
  tempStructPts->GetSpacing(Spacing);

  dims[2] = (imageRange[1] - imageRange[0] + 1);

  if ((dims[0] * dims[1] * dims[2]) <= 1 || dims[2] < 2)
  {
    vtkErrorMacro(<< "Bad dimensions...slice must be 3D volume");
    fclose(outFP);
    return;
  }

  xmin[0] = xmin[1] = xmin[2] = VTK_DOUBLE_MAX;
  xmax[0] = xmax[1] = xmax[2] = -VTK_DOUBLE_MAX;

  inScalars = tempStructPts->GetPointData()->GetScalars();
  if (inScalars == nullptr)
  {
    vtkErrorMacro(<< "Must have scalars to generate isosurface");
    tempStructPts->Delete();
    fclose(outFP);
    return;
  }
  inScalars->Register(this);
  tempStructPts->Delete();

  if (inScalars->GetNumberOfComponents() == 1)
  {
    switch (inScalars->GetDataType())
    {
      case VTK_CHAR:
      {
        vtkCharArray* scalars = (vtkCharArray*)inScalars;
        char* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_UNSIGNED_CHAR:
      {
        vtkUnsignedCharArray* scalars = (vtkUnsignedCharArray*)inScalars;
        unsigned char* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_SHORT:
      {
        vtkShortArray* scalars = (vtkShortArray*)inScalars;
        short* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_UNSIGNED_SHORT:
      {
        vtkUnsignedShortArray* scalars = (vtkUnsignedShortArray*)inScalars;
        unsigned short* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_INT:
      {
        vtkIntArray* scalars = (vtkIntArray*)inScalars;
        int* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_UNSIGNED_INT:
      {
        vtkUnsignedIntArray* scalars = (vtkUnsignedIntArray*)inScalars;
        unsigned int* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_LONG:
      {
        vtkLongArray* scalars = (vtkLongArray*)inScalars;
        long* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_UNSIGNED_LONG:
      {
        vtkUnsignedLongArray* scalars = (vtkUnsignedLongArray*)inScalars;
        unsigned long* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_FLOAT:
      {
        vtkFloatArray* scalars = (vtkFloatArray*)inScalars;
        float* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
      case VTK_DOUBLE:
      {
        vtkDoubleArray* scalars = (vtkDoubleArray*)inScalars;
        double* s = scalars->GetPointer(0);
        vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
          outFP, this->Reader, this->Debug);
      }
      break;
    } // switch
  }

  else // multiple components have to convert
  {
    vtkDoubleArray* scalars = (vtkDoubleArray*)inScalars;
    double* s = nullptr; // clue to convert data to double
    vtkSliceCubesContour(s, scalars, imageRange, dims, origin, Spacing, this->Value, xmin, xmax,
      outFP, this->Reader, this->Debug);
  }

  inScalars->UnRegister(this);

  if (this->LimitsFileName)
  {
    int i;
    float t;

    if ((outFP = vtksys::SystemTools::Fopen(this->LimitsFileName, "wb")) == nullptr)
    {
      vtkWarningMacro(<< "Sorry, couldn't write limits file...");
    }
    else
    {
      bool status = true;
      float forigin[3];
      for (i = 0; i < 3 && status; i++)
      {
        t = origin[i] + (dims[i] - 1) * Spacing[i];
        forigin[i] = (float)origin[i];
        status = vtkByteSwap::SwapWrite4BERange(forigin + i, 1, outFP);
        if (!status)
        {
          vtkWarningMacro(<< "SwapWrite failed.");
        }
        // swap if necessary
        if (status)
        {
          status = vtkByteSwap::SwapWrite4BERange(&t, 1, outFP);
          if (!status)
          {
            vtkWarningMacro(<< "SwapWrite failed.");
          }
        }
      }
      float ftmp;
      for (i = 0; i < 3 && status; i++)
      {
        ftmp = (float)xmin[i];
        status = vtkByteSwap::SwapWrite4BERange(&ftmp, 1, outFP);
        if (!status)
        {
          vtkWarningMacro(<< "SwapWrite failed.");
        }
        ftmp = (float)xmax[i];
        if (status)
        {
          status = vtkByteSwap::SwapWrite4BERange(&ftmp, 1, outFP);
          if (!status)
          {
            vtkWarningMacro(<< "SwapWrite failed.");
          }
        }
      }
    }
    fclose(outFP);
  }
}

void vtkSliceCubes::PrintSelf(ostream& os, vtkIndent indent)
{
  this->Superclass::PrintSelf(os, indent);

  os << indent << "Iso Value: " << this->Value << "\n";

  if (this->Reader)
  {
    os << indent << "Reader:\n";
    this->Reader->PrintSelf(os, indent.GetNextIndent());
  }
  else
  {
    os << indent << "Reader: (none)\n";
  }

  os << indent << "File Name: " << (this->FileName ? this->FileName : "(none)") << "\n";
  os << indent << "Limits File Name: " << (this->LimitsFileName ? this->LimitsFileName : "(none)")
     << "\n";
}
